Table Of ContentMethods in
Molecular Biology 1087
Elisa Vicenzi
Guido Poli Editors
Human
Retroviruses
Methods and Protocols
M M B ™
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
http://www.springer.com/series/7651
Human Retroviruses
Methods and Protocols
Edited by
Elisa Vicenzi and Guido Poli
Division of Immunology, Transplant, and Infectious Diseases,
San Raffaele Scientific Institute, Milano, Italy
Editors
Elisa Vicenzi Guido Poli
Division of Immunology, Transplant, Division of Immunology, Transplant,
and Infectious Diseases and Infectious Diseases
San Raffaele Scientific Institute San Raffaele Scientific Institute
Milano , I taly Milano, Italy
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-62703-669-6 ISBN 978-1-62703-670-2 (eBook)
DOI 10.1007/978-1-62703-670-2
Springer New York Heidelberg Dordrecht London
Library of Congress Control Number: 2013949423
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Dedication
( Excerpt from the obituary published in “Retrovirology” by Ben Berkhout et al.,
Retrovirology, 2013 Mar 21; 10:28 )
Our friend Kuan-Teh Jeang, “Teh” to friends and colleagues, passed away unexpectedly at
the age of 54 on the evening of January 27, 2013. Great shock and sorrow rapidly spread
through the scientifi c community all over the world.
Teh was born in 1958 in Taiwan and went to the US in 1970. At age 16, he began col-
lege at the Massachusetts Institute of Technology and, after two years, started medical
school at the “Johns Hopkins” University in Baltimore, receiving both his M.D. and Ph.D.
degrees by age 25. During his time at Hopkins, Teh met his wife, Diane, a graduate student
in the same laboratory. They married in 1984 in Iowa, where Teh completed his medical
internship. The next year, Teh started his postdoctoral work at the NIH in the laboratory
of Dr. George Khoury, NCI.
Teh had been working at the NIH in Bethesda for 27 years, exactly half of his life, as
Chief of the Molecular Virology Section in the Laboratory of Molecular Microbiology
directed by Malcolm A. Martin. His major research interest was around the human immu-
nodefi ciency virus (HIV-1 ) and the human T-cell leukemia virus (HTLV-I), contributing
with >300 scientifi c papers, some of which of seminal relevance and published in the best
scientifi c journals. He stopped bench working only in 2004 when he became editor-in-chief
of Retrovirology .
In the late 1980s, Teh showed that HIV-1 uses an unprecedented mechanism of tran-
scription that is dictated by an RNA-binding protein, Tat, which binds a nascent viral RNA
target (TAR), the fi rst RNA enhancer element ever described. Subsequently, Teh’s group
characterized cellular RNA-binding proteins that regulate HIV-1 replication, including the
TAR RNA-b inding protein (TRBP) that later became known as an important factor of the
cellular RNA interference machinery. In recent work, his lab completed a genome-wide
screening for human cell factors that are needed for HIV-1 replication. Using novel tech-
nology, Teh extended his interests in RNA-biology through the identifi cation of small
RNAs (i.e., siRNAs and miRNAs) that have biologically important roles in viral infection,
cellular metabolism, and virus-induced pathogenesis.
In addition to all his scientifi c achievements, one of Teh’s greatest contributions to sci-
ence has been his role as mentor for young scientists who have since spread across the
globe, from Taiwan to China, from France to the Netherlands, and from Canada to many
places in the United States. His mentoring commitment is also refl ected in his service to
many professional societies and in his special interest in the area of scientifi c publication.
From the earliest years, Teh was an advocate of the Open Access publishing format (“ science
should be free as oxygen in the air…” was used to say presenting the initiative). In 2004
he launched, as Editor-in-Chief, the journal R etrovirology that became, in less than 10 years,
among the highest cited journals in the fi eld of virology. After R etrovirology , Teh pushed
vi Dedication
for more journal involvement with the retroviral community … and F rontiers in Retrovirology
was born in 2009 along with the fi rst and very successful conference organized by BioMed
Central in Montpellier, France.
Teh was also a true scientifi c leader, initiating scientifi c debate, writing editorials, sitting
on many committees, orchestrating new book volumes, and organizing international meet-
ings on diverse topics. For instance, he was President of the Society of Chinese Bioscientists
in America (SCBA) in 2010 and voiced the strong opinion that the representation of Asian-
American scientists in leadership positions should be increased.
Teh was the recipient of many awards, most recently the International Retrovirology
Association’s Dale McFarlin Award in 2011, BioMed Central’s Open Access “Editor of the
Year” in 2010 and the Johns Hopkins University Woodrow Wilson Award in 2009. Teh was
also elected to membership in prestigious societies such as the Academia Sinica in Taiwan,
Fellow of the American Academy of Microbiology, and Fellow of the American Association
for the Advancement of Science.
Teh had an infectious enthusiasm and winner’s mentality both at work and play. He was
a skilled tennis and chess player, a gifted writer, and a great debater with strong opinions on
virtually all subjects of science and life. Additionally, he had a passion for current events and
a love for travel, movies, food, and music.
Teh’s death is a blow to the retrovirus research community and we will sorely miss his
scientifi c leadership. He has been central to so much of what we have accomplished together
as well as being a supportive and generous friend to many of us individually.
Teh’s life was much too short, but his legacy and our memories of him will last forever.
Our hearts and condolences are with his wife Diane and his three children David (23),
Diana (20), and John (15). This book is dedicated to him and his untamed enthusiasm for
science and life.
In the Deserved Honor of Kuan-Teh Jeang,
a Visionary in Science and Communication
By Jean-Luc Darlix
Dear Teh,
We’ll miss you
Yes, we’ll miss you so much,
We’ll miss your ideas and unforgettable dedications
In Science while constantly advocating for novel communications,
Debating with enthusiasm for worldwide free open access,
So brightly, straightforwardly with fairness.
Yes, Dear Teh
We’ll miss all of these original views of Yours
At the very same time
We’ll miss the man
Yes, the Man
Dedication vii
viii Dedication
1 . Ajit Kumar, Teh, Michael Bukrinski and Rakesh Kumar at George Washington University,
Washington DC, ca. January 19, 2013.
2. Juang Jeng-Tse, Teh, Jeremy Luban and Guido Poli, San Raffaele Scientific Institute,
Milano, 2008.
3. Teh and Jean Luc Darlix in Lyon Fourvière, France, June 2011.
4. Teh and Anne Napoly in Lyon Fourvière, France, June 2011.
5. Teh giving giving the Retrovirology Achievement Award to JL Darlix, June 2011.
6. Anna Cereseto and Teh, San Raffaele Scientific Institute, Milano, 2008.
7. Teh presenting the Open Access experience as Editor-in-Chief of “Retrovirology.”
8. Gabriella Scarlatti and Teh at the International Conference on HIV/AIDS in Vienna,
Austria, 2010.
9. Diane Havlir and Teh at the International Conference on HIV/AIDS in Vienna, Austria,
2010.
10. Teh and the Editors of Retrovirology Monsef Benkirane (left) and Ben Berkhout (right) at
the International Conference on HIV/AIDS in Vienna, Austria, 2010.
Pref ace
There are several books on HIV/AIDS and retrovirology dedicated to either basic virology,
immunology or the clinical and social aspects of this pandemic infectious disease. So, why
another book on this subject! Because, this is the fi rst collection of articles dedicated to the
key experimental protocols that are at the basis of all the major discoveries of the fi eld since
pathogenic human retroviruses came under the limelight with human T-cell leukemia/
lymphoma virus type 1 (HTLV-1) in 1980—a virus causing the rare adult T cell leukemia
and tropical spastic paraparesis—and, especially, with the discovery of the human immuno-
defi ciency virus type 1 (HIV-1) in 1983–1984 and HIV-2 (1986) as the etiological agents
of the acquired immunodefi ciency syndrome (AIDS), still a major threat to mankind with
more than 34 millions infections worldwide and 7,500 new infections daily.
The current book is organized in 5 blocks of chapters focusing on the following:
“Mapping the HIV life cycle” (14 chapters), “Isolation, co-receptor use, and cell tropism
of HIV-1” (5 chapters), “In vivo quantifi cation of HIV-1” (2 chapters), “Biological aspects
of HIV-1” (2 chapters) and, last, but not least, to “HTLVs” (3 chapters).
Of course, most of the chapters are dedicated to HIV-1, the big killer, but there are also
issues dedicated to HIV-2 and to the HTLVs, including the still “disease-less” HTLV-2. In
addition, some articles explore “assay and function of accessory genes,” largely involving
the interface between retroviral and host factors, the extracellular role of Tat and Tax,
resembling the function of cytokines, and the biotechnological exploitation of HIV as len-
tiviral vector to carry foreign genes with therapeutic value.
Although the “core business” of the book and of its individual chapters is to provide
state-of-art methodological protocols from world leaders in human retrovirology, the book
is not meant to be a just a collection of “cook-book recipes.” In fact, each chapter provides
an updated, though synthetic, review of the fundamental knowledge concerning a single
retroviral life step.
Enjoy reading!
Milano, Italy Elisa Vicenzi
Guido Poli
ix
